PyImageJ Documentation Revitalization
- Dominant language
- Python
- Stars
- 534
- Forks
- 95
- PR merge metrics
- No merged PRs in 30d
Description
I decided to start one parent issue for documentation which can be updated with other documentation improvements.
Things I've noticed:
- [ ] The [Troubleshooting notebook](https://github.com/imagej/pyimagej/blob/main/doc/12-Troubleshooting.ipynb) is not in sync with the [Troubleshooting page](https://github.com/imagej/pyimagej/blob/main/doc/Troubleshooting.md)
- [ ] [Integration](https://github.com/imagej/pyimagej/blob/main/doc/integration-use-cases.rst) doesn't mention [napari-imagej](https://napari.imagej.net/en/stable/)
- [ ] Initialization --> "with more memory" feels like it is contradicting the "configuring the JVM". Clarify when to use one or the other.
- [ ] Make the "Ways to initialize" table fit without horizontal scrollbars
- [ ] "Tutorial notebooks" would benefit from an "open in colab" option/better interactivity. Is there a way to embed in RTD?
- [ ] `Blob detection (interactive)` uses napari??
- [ ] "Troubleshooting -> Common Errors" would benefit from separation of scope (user, developer)
- [ ] Some examples do not use [reproducible initialization](https://github.com/imagej/pyimagej/blob/74d7d2210201d3523d208a2b5793e08e0a92c4aa/doc/examples/blob_detection_xvfb.py#L71)
- [ ] Update examples to not use wsr.imagej.net
- [ ] 6.2 is broken?
- [ ] All the Ops stuff is ImageJ Ops and should probably be removed
- [ ] https://py.imagej.net/en/latest/Cellpose-StarDist-Segmentation.html needs work (version pins)
- [ ] Improve [headless instructions](https://py.imagej.net/en/latest/Headless.html#using-pyimagej-with-xvfb) with subprocess.Popen(["Xvfb", ":99", "-screen", "0", "1024x768x24"]) and a clearer explanation of **when** headless mode is really needed
- [x] All installation instructions need to be updated to use `uv`
Related issues:
* https://github.com/imagej/pyimagej/issues/331
* https://github.com/imagej/pyimagej/issues/332
Contributor guide
No contributing guide indexed for this repository
Research direction
Review doc/12-Troubleshooting.ipynb alongside doc/Troubleshooting.md, integration-use-cases.rst, and the linked headless and segmentation pages; use related issues 331 and 332 as context. Break the parent into focused documentation tasks, then verify each listed discrepancy and instruction update is reflected in the relevant docs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100